diff --git a/fsl/fsleyes/gl/annotations.py b/fsl/fsleyes/gl/annotations.py
index 06b9a42b820fbcc75832b3751f86d8b8c858b5f9..e73348e827acb1be0bf7bd7a78bf9d94ed007c2b 100644
--- a/fsl/fsleyes/gl/annotations.py
+++ b/fsl/fsleyes/gl/annotations.py
@@ -95,21 +95,27 @@ class Annotations(object):
def line(self, *args, **kwargs):
"""Queues a line for drawing - see the :class:`Line` class. """
hold = kwargs.pop('hold', False)
- return self.obj(Line(*args, **kwargs), hold)
+ obj = Line(self.__xax, self.__yax, *args, **kwargs)
+
+ return self.obj(obj, hold)
def rect(self, *args, **kwargs):
"""Queues a rectangle for drawing - see the :class:`Rectangle` class.
"""
hold = kwargs.pop('hold', False)
- return self.obj(Rect(*args, **kwargs), hold)
+ obj = Rect(self.__xax, self.__yax, *args, **kwargs)
+
+ return self.obj(obj, hold)
def grid(self, *args, **kwargs):
"""Queues a voxel grid for drawing - see the :class:`VoxelGrid` class.
"""
hold = kwargs.pop('hold', False)
- return self.obj(VoxelGrid(*args, **kwargs), hold)
+ obj = VoxelGrid(self.__xax, self.__yax, *args, **kwargs)
+
+ return self.obj(obj, hold)
def selection(self, *args, **kwargs):
@@ -117,7 +123,9 @@ class Annotations(object):
class.
"""
hold = kwargs.pop('hold', False)
- return self.obj(VoxelSelection(*args, **kwargs), hold)
+ obj = VoxelSelection(self.__xax, self.__yax, *args, **kwargs)
+
+ return self.obj(obj, hold)
def obj(self, obj, hold=False):
@@ -236,9 +244,13 @@ class AnnotationObject(globject.GLSimpleObject):
:meth:`globject.GLObject.draw` method.
"""
- def __init__(self, xform=None, colour=None, width=None):
+ def __init__(self, xax, yax, xform=None, colour=None, width=None):
"""Create an ``AnnotationObject``.
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
+
:arg xform: Transformation matrix which will be applied to all
vertex coordinates.
@@ -246,7 +258,7 @@ class AnnotationObject(globject.GLSimpleObject):
:arg width: Line width to use for the annotation.
"""
- globject.GLSimpleObject.__init__(self)
+ globject.GLSimpleObject.__init__(self, xax, yax)
self.colour = colour
self.width = width
@@ -269,13 +281,17 @@ class Line(AnnotationObject):
2D line.
"""
- def __init__(self, xy1, xy2, *args, **kwargs):
+ def __init__(self, xax, yax, xy1, xy2, *args, **kwargs):
"""Create a ``Line`` annotation.
The ``xy1`` and ``xy2`` coordinate tuples should be in relation to the
axes which map to the horizontal/vertical screen axes on the target
canvas.
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
+
:arg xy1: Tuple containing the (x, y) coordinates of one endpoint.
:arg xy2: Tuple containing the (x, y) coordinates of the second
@@ -284,7 +300,7 @@ class Line(AnnotationObject):
All other arguments are passed through to
:meth:`AnnotationObject.__init__`.
"""
- AnnotationObject.__init__(self, *args, **kwargs)
+ AnnotationObject.__init__(self, xax, yax, *args, **kwargs)
self.xy1 = xy1
self.xy2 = xy2
@@ -310,18 +326,22 @@ class Rect(AnnotationObject):
2D rectangle.
"""
- def __init__(self, xy, w, h, *args, **kwargs):
+ def __init__(self, xax, yax, xy, w, h, *args, **kwargs):
"""Create a :class:`Rect` annotation.
- :arg xy: Tuple specifying bottom left of the rectangle, in the display
- coordinate system.
- :arg w: Rectangle width.
- :arg h: Rectangle height.
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
+
+ :arg xy: Tuple specifying bottom left of the rectangle, in the display
+ coordinate system.
+ :arg w: Rectangle width.
+ :arg h: Rectangle height.
All other arguments are passed through to
:meth:`AnnotationObject.__init__`.
"""
- AnnotationObject.__init__(self, *args, **kwargs)
+ AnnotationObject.__init__(self, xax, yax, *args, **kwargs)
self.xy = xy
self.w = w
self.h = h
@@ -371,6 +391,8 @@ class VoxelGrid(AnnotationObject):
def __init__(self,
+ xax,
+ yax,
selectMask,
displayToVoxMat,
voxToDisplayMat,
@@ -379,6 +401,10 @@ class VoxelGrid(AnnotationObject):
**kwargs):
"""Create a ``VoxelGrid`` annotation.
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
+
:arg selectMask: A 3D numpy array, the same shape as the image
being annotated (or a sub-space of the image -
see the ``offsets`` argument), which is
@@ -403,7 +429,7 @@ class VoxelGrid(AnnotationObject):
"""
kwargs['xform'] = voxToDisplayMat
- AnnotationObject.__init__(self, *args, **kwargs)
+ AnnotationObject.__init__(self, xax, yax, *args, **kwargs)
if offsets is None:
offsets = [0, 0, 0]
@@ -453,6 +479,8 @@ class VoxelSelection(AnnotationObject):
def __init__(self,
+ xax,
+ yax,
selection,
displayToVoxMat,
voxToDisplayMat,
@@ -461,6 +489,10 @@ class VoxelSelection(AnnotationObject):
**kwargs):
"""Create a ``VoxelSelection`` annotation.
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
+
:arg selection: A :class:`.Selection` instance which defines
the voxels to be highlighted.
@@ -484,7 +516,7 @@ class VoxelSelection(AnnotationObject):
:meth:`AnnotationObject.__init__` method.
"""
- AnnotationObject.__init__(self, *args, **kwargs)
+ AnnotationObject.__init__(self, xax, yax, *args, **kwargs)
if offsets is None:
offsets = [0, 0, 0]
diff --git a/fsl/fsleyes/gl/gllabel.py b/fsl/fsleyes/gl/gllabel.py
index b01e27ad31bcd4d451cdff23f2312001def1cc39..a33ecb0a1d4091846d31f72ae6548d753e3a164a 100644
--- a/fsl/fsleyes/gl/gllabel.py
+++ b/fsl/fsleyes/gl/gllabel.py
@@ -43,20 +43,25 @@ class GLLabel(globject.GLImageObject):
"""
- def __init__(self, image, display):
+ def __init__(self, image, display, xax, yax):
"""Create a ``GLLabel``.
:arg image: The :class:`.Image` instance.
:arg display: The associated :class:`.Display` instance.
+ :arg xax: Initial display X axis
+ :arg yax: Initial display Y axis
"""
- globject.GLImageObject.__init__(self, image, display)
-
- lutTexName = '{}_lut'.format(self.name)
+ globject.GLImageObject.__init__(self, image, display, xax, yax)
+ lutTexName = '{}_lut'.format(self.name)
self.lutTexture = textures.LookupTableTexture(lutTexName)
self.imageTexture = None
+ # The shader attribute will be created
+ # by the gllabel_funcs module
+ self.shader = None
+
self.addListeners()
self.refreshLutTexture()
@@ -86,7 +91,9 @@ class GLLabel(globject.GLImageObject):
"""Returns ``True`` if this ``GLLabel`` is ready to be drawn, ``False``
otherwise.
"""
- return self.imageTexture is not None and self.imageTexture.ready()
+ return self.shader is not None and \
+ self.imageTexture is not None and \
+ self.imageTexture.ready()
def addListeners(self):
diff --git a/fsl/fsleyes/gl/gllinevector.py b/fsl/fsleyes/gl/gllinevector.py
index 1549f9bdd5e9eb1313455054f429d2668b074814..fce6f809f1bc95820a2b9e1ac1850031ec482309 100644
--- a/fsl/fsleyes/gl/gllinevector.py
+++ b/fsl/fsleyes/gl/gllinevector.py
@@ -53,12 +53,13 @@ class GLLineVector(glvector.GLVector):
"""
- def __init__(self, image, display):
+ def __init__(self, image, display, xax, yax):
"""Create a ``GLLineVector`` instance.
:arg image: An :class:`.Image` or :class:`.TensorImage` instance.
-
:arg display: The associated :class:`.Display` instance.
+ :arg xax: Initial display X axis
+ :arg yax: Initial display Y axis
"""
# If the overlay is a TensorImage, use the
@@ -70,6 +71,8 @@ class GLLineVector(glvector.GLVector):
glvector.GLVector.__init__(self,
image,
display,
+ xax,
+ yax,
vectorImage=vecImage,
init=lambda: fslgl.gllinevector_funcs.init(
self))
diff --git a/fsl/fsleyes/gl/glmodel.py b/fsl/fsleyes/gl/glmodel.py
index 0dd61055d9b2631825d14e2eab06a83d2104b9b2..0e348889ee4716e777f7d36b571e24ed68c7e74b 100644
--- a/fsl/fsleyes/gl/glmodel.py
+++ b/fsl/fsleyes/gl/glmodel.py
@@ -65,16 +65,20 @@ class GLModel(globject.GLObject):
"""
- def __init__(self, overlay, display):
+ def __init__(self, overlay, display, xax, yax):
"""Create a ``GLModel``.
:arg overlay: A :class:`.Model` overlay.
:arg display: A :class:`.Display` instance defining how the
``overlay`` is to be displayed.
+
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
"""
- globject.GLObject.__init__(self)
+ globject.GLObject.__init__(self, xax, yax)
self.shader = None
self.overlay = overlay
diff --git a/fsl/fsleyes/gl/globject.py b/fsl/fsleyes/gl/globject.py
index 3c03d030e594c6b14bb1c216246b07a4e20bd83b..72fbc67e0dfc7730cdc7c262d8f5179be7afcd52 100644
--- a/fsl/fsleyes/gl/globject.py
+++ b/fsl/fsleyes/gl/globject.py
@@ -50,7 +50,7 @@ def getGLObjectType(overlayType):
return typeMap.get(overlayType, None)
-def createGLObject(overlay, display):
+def createGLObject(overlay, display, xax, yax):
"""Create :class:`GLObject` instance for the given overlay, as specified
by the :attr:`.Display.overlayType` property.
@@ -58,10 +58,14 @@ def createGLObject(overlay, display):
:arg display: A :class:`.Display` instance describing how the overlay
should be displayed.
+
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
"""
ctr = getGLObjectType(display.overlayType)
- if ctr is not None: return ctr(overlay, display)
+ if ctr is not None: return ctr(overlay, display, xax, yax)
else: return None
@@ -104,7 +108,11 @@ class GLObject(notifier.Notifier):
Sub-class implementations must do the following:
- - Call :meth:`__init__`.
+ - Call :meth:`__init__`. A ``GLObject.__init__`` sub-class method must
+ have the following signature::
+
+ def __init__(self, overlay, display, xax, yax)
+
- Call :meth:`notify` whenever its OpenGL representation changes.
@@ -132,23 +140,26 @@ class GLObject(notifier.Notifier):
"""
- def __init__(self):
- """Create a :class:`GLObject`. The constructor adds one attribute
+ def __init__(self, xax, yax):
+ """Create a :class:`GLObject`. The constructor adds one attribute
to this instance, ``name``, which is simply a unique name for this
- instance, and gives default values to the ``xax``, ``yax``, and
- ``zax`` attributes.
+ instance, and gives values to the ``xax``, ``yax``, and ``zax``
+ attributes.
Subclass implementations must call this method, and should also
perform any necessary OpenGL initialisation, such as creating
textures.
+
+ :arg xax: Initial display X axis
+ :arg yax: Initial display Y axis
"""
# Give this instance a name, and set
# initial values for the display axes
self.name = '{}_{}'.format(type(self).__name__, id(self))
- self.xax = 0
- self.yax = 1
- self.zax = 2
+ self.xax = xax
+ self.yax = yax
+ self.zax = 3 - xax - yax
log.memory('{}.init ({})'.format(type(self).__name__, id(self)))
@@ -285,9 +296,9 @@ class GLSimpleObject(GLObject):
be called.
"""
- def __init__(self):
+ def __init__(self, xax, yax):
"""Create a ``GLSimpleObject``. """
- GLObject.__init__(self)
+ GLObject.__init__(self, xax, yax)
def ready(self):
@@ -315,7 +326,7 @@ class GLImageObject(GLObject):
of :class:`.Nifti1` instances.
"""
- def __init__(self, image, display):
+ def __init__(self, image, display, xax, yax):
"""Create a ``GLImageObject``.
This constructor adds the following attributes to this instance:
@@ -333,9 +344,13 @@ class GLImageObject(GLObject):
:arg image: The :class:`.Nifti1` instance
:arg display: An associated :class:`.Display` instance.
+
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
"""
- GLObject.__init__(self)
+ GLObject.__init__(self, xax, yax)
self.image = image
self.display = display
self.displayOpts = display.getDisplayOpts()
diff --git a/fsl/fsleyes/gl/glrgbvector.py b/fsl/fsleyes/gl/glrgbvector.py
index 5d290dd506ace290f48abe8b9bebda278f5970ad..4c25bd4f51f9639617c81ad32f3d6120c65e4420 100644
--- a/fsl/fsleyes/gl/glrgbvector.py
+++ b/fsl/fsleyes/gl/glrgbvector.py
@@ -59,11 +59,13 @@ class GLRGBVector(glvector.GLVector):
"""
- def __init__(self, image, display):
+ def __init__(self, image, display, xax, yax):
"""Create a ``GLRGBVector``.
:arg image: An :class:`.Image` or :class:`.TensorImage` instance.
:arg display: The associated :class:`.Display` instance.
+ :arg xax: Initial display X axis
+ :arg yax: Initial display Y axis
"""
# If the overlay is a TensorImage, use the
@@ -75,6 +77,8 @@ class GLRGBVector(glvector.GLVector):
glvector.GLVector.__init__(self,
image,
display,
+ xax,
+ yax,
prefilter=np.abs,
vectorImage=vecImage,
init=lambda: fslgl.glrgbvector_funcs.init(
diff --git a/fsl/fsleyes/gl/gltensor.py b/fsl/fsleyes/gl/gltensor.py
index 96f8e7d68bbd91d840a1136ea41e9baf33005279..064adc63da314730aa0fc9fe847cfafa28de6ec5 100644
--- a/fsl/fsleyes/gl/gltensor.py
+++ b/fsl/fsleyes/gl/gltensor.py
@@ -28,7 +28,7 @@ class GLTensor(glvector.GLVector):
"""
- def __init__(self, image, display):
+ def __init__(self, image, display, xax, yax):
"""Create a ``GLTensor``. Calls the :func:`.gl21.gltensor_funcs.init`
function.
@@ -36,10 +36,16 @@ class GLTensor(glvector.GLVector):
:arg display: The :class:`.Display` instance associated with the
``image``.
+
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
"""
glvector.GLVector.__init__(self,
image,
display,
+ xax,
+ yax,
prefilter=np.abs,
vectorImage=image.V1(),
init=lambda: fslgl.gltensor_funcs.init(
diff --git a/fsl/fsleyes/gl/glvector.py b/fsl/fsleyes/gl/glvector.py
index a05935eff28486b9befa3428c0df3ed63b7242e6..f47b6fc7a64423e5123da84baa999727b569cb11 100644
--- a/fsl/fsleyes/gl/glvector.py
+++ b/fsl/fsleyes/gl/glvector.py
@@ -96,6 +96,8 @@ class GLVector(globject.GLImageObject):
def __init__(self,
image,
display,
+ xax,
+ yax,
prefilter=None,
vectorImage=None,
init=None):
@@ -116,6 +118,10 @@ class GLVector(globject.GLImageObject):
:arg display: A :class:`.Display` object which describes how the
image is to be displayed.
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
+
:arg prefilter: An optional function which filters the data before it
is stored as a 3D texture. See
:class:`.ImageTexture`. Whether or not this function
@@ -145,7 +151,7 @@ class GLVector(globject.GLImageObject):
raise ValueError('Image must be 4 dimensional, with 3 volumes '
'representing the XYZ vector angles')
- globject.GLImageObject.__init__(self, image, display)
+ globject.GLImageObject.__init__(self, image, display, xax, yax)
name = self.name
diff --git a/fsl/fsleyes/gl/glvolume.py b/fsl/fsleyes/gl/glvolume.py
index e04fa19dde427adec8045e175daf1044bbc8dde1..3eb8125ac25889f55ea633c6b813993eed9d02bb 100644
--- a/fsl/fsleyes/gl/glvolume.py
+++ b/fsl/fsleyes/gl/glvolume.py
@@ -142,16 +142,20 @@ class GLVolume(globject.GLImageObject):
"""
- def __init__(self, image, display):
+ def __init__(self, image, display, xax, yax):
"""Create a ``GLVolume`` object.
:arg image: An :class:`.Image` object.
:arg display: A :class:`.Display` object which describes how the image
is to be displayed.
+
+ :arg xax: Initial display X axis
+
+ :arg yax: Initial display Y axis
"""
- globject.GLImageObject.__init__(self, image, display)
+ globject.GLImageObject.__init__(self, image, display, xax, yax)
# Add listeners to this image so the view can be
# updated when its display properties are changed
diff --git a/fsl/fsleyes/gl/slicecanvas.py b/fsl/fsleyes/gl/slicecanvas.py
index 0b3d700d17f916fdf69433430243e8093bbfbf12..5ce14d3dfaeec264e907b2c60285a78162f84ec4 100644
--- a/fsl/fsleyes/gl/slicecanvas.py
+++ b/fsl/fsleyes/gl/slicecanvas.py
@@ -802,10 +802,12 @@ class SliceCanvas(props.HasProperties):
self._glObjects.pop(overlay)
return
- globj = globject.createGLObject(overlay, display)
+ globj = globject.createGLObject(overlay,
+ display,
+ self.xax,
+ self.yax)
if globj is not None:
- globj.setAxes(self.xax, self.yax)
globj.register(self.name, self._refresh)
self._glObjects[overlay] = globj